Likelihood-Based Inference for Discretely Observed Birth-Death-Shift Processes, with Applications to Evolution of Mobile Genetic Elements

Continuous-time birth-death-shift (BDS) processes are frequently used in stochastic modeling, with many applications in ecology and epidemiology. In particular, such processes can model evolutionary dynamics of transposable elements - important genetic markers in molecular epidemiology. Estimation of the effects of individual covariates on the birth, death, and shift rates of the process can be accomplished by analyzing patient data, but inferring these rates in a discretely and unevenly observed setting presents computational challenges. We propose a mutli-type branching process approximation to BDS processes and develop a corresponding expectation maximization (EM) algorithm, where we use spectral techniques to reduce calculation of expected sufficient statistics to low dimensional integration. These techniques yield an efficient and robust optimization routine for inferring the rates of the BDS process, and apply more broadly to multi-type branching processes where rates can depend on many covariates. After rigorously testing our methodology in simulation studies, we apply our method to study intrapatient time evolution of IS6110 transposable element, a frequently used element during estimation of epidemiological clusters of Mycobacterium tuberculosis infections.Comment: 31 pages, 7 figures, 1 tabl

Efficient Transition Probability Computation for Continuous-Time Branching Processes via Compressed Sensing

Branching processes are a class of continuous-time Markov chains (CTMCs) with ubiquitous applications. A general difficulty in statistical inference under partially observed CTMC models arises in computing transition probabilities when the discrete state space is large or uncountable. Classical methods such as matrix exponentiation are infeasible for large or countably infinite state spaces, and sampling-based alternatives are computationally intensive, requiring a large integration step to impute over all possible hidden events. Recent work has successfully applied generating function techniques to computing transition probabilities for linear multitype branching processes. While these techniques often require significantly fewer computations than matrix exponentiation, they also become prohibitive in applications with large populations. We propose a compressed sensing framework that significantly accelerates the generating function method, decreasing computational cost up to a logarithmic factor by only assuming the probability mass of transitions is sparse. We demonstrate accurate and efficient transition probability computations in branching process models for hematopoiesis and transposable element evolution.Comment: 18 pages, 4 figures, 2 table

Asymptotic stability for neural networks with mixed time-delays: The discrete-time case

This is the post print version of the article. The official published version can be obtained from the link - Copyright 2009 Elsevier LtdThis paper is concerned with the stability analysis problem for a new class of discrete-time recurrent neural networks with mixed time-delays. The mixed time-delays that consist of both the discrete and distributed time-delays are addressed, for the first time, when analyzing the asymptotic stability for discrete-time neural networks. The activation functions are not required to be differentiable or strictly monotonic. The existence of the equilibrium point is first proved under mild conditions. By constructing a new Lyapnuov–Krasovskii functional, a linear matrix inequality (LMI) approach is developed to establish sufficient conditions for the discrete-time neural networks to be globally asymptotically stable. As an extension, we further consider the stability analysis problem for the same class of neural networks but with state-dependent stochastic disturbances. All the conditions obtained are expressed in terms of LMIs whose feasibility can be easily checked by using the numerically efficient Matlab LMI Toolbox. A simulation example is presented to show the usefulness of the derived LMI-based stability condition.This work was supported in part by the Biotechnology and Biological Sciences Research Council (BBSRC) of the UK under Grants BB/C506264/1 and 100/EGM17735, the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grants GR/S27658/01 and EP/C524586/1, an International Joint Project sponsored by the Royal Society of the UK, the Natural Science Foundation of Jiangsu Province of China under Grant BK2007075, the National Natural Science Foundation of China under Grant 60774073, and the Alexander von Humboldt Foundation of Germany